Skip to main content

Table 3 Reaction network of the heat shock response model.

From: A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks

RxnNo. Reactions Rate const Reaction Type
1 Protein → UnfProt 0.2 Unfolding
2 UnfProt + DnaJ → UnfProt:DnaJ 0.0108 Association
3 UnfProt:DnaJ → Protein + DnaJ 0.2 Dissociation/Folding
4 DNA(σ32) → mRNA(σ32) 1.40E-03 Transcription
5 mRNA(σ32) → σ32 0.07 Translation
6 mRNA(σ32) → degrades 1.40E-06 Degradation
7 σ32 → σ32RNAP 0.7 Conformational
8 σ32RNAP → σ32 1.3E-01 Conformational
9 DNA(DnaJ) + σ32RNAP → DNA(DnaJ) + σ32 + DnaJ 4.88E-03 Transcription combined with Translation
10 DNA(FtsH) + σ32RNAP → DNA(FtsH) + σ32 + FtsH 4.88E-03  
11 DNA(GroEL) + σ32RNAP → DNA(GroEL) + σ32 + GroEL 6.29E-03  
12 DnaJ → degrades 6.40E-10 Degradation
13 FtsH → degrades 7.40E-11  
14 GroEL → degrades 1.80E-08  
15 σ32 + DnaJ → σ32:DnaJ 3.62E-04 Association
16 σ32:DnaJ → σ32 + DnaJ 4.40E-04 Dissociation
17 FtsH + σ32:DnaJ → DnaJ + FtsH 1.42E-06  
  1. The units of stochastic rate constants are s-1 for 1st-order reactions and (molecule-s)-1 for 2nd-order reactions. DNA(X) and mRNA(X) correspond to DNA sequence and mRNA transcripts, respectively, for species X. DNA (or mRNA) molecules do not get consumed in the transcription (or translation) reactions, but simply provide a template for mRNA (or protein) formation.